TB-Profiler result

Run: SRR17567917
Summary

Run ID: SRR17567917

Sample name:

Date: 2024-04-13T22:33:15.855624

Number of reads: 2666905

Percentage reads mapped: 75.02

Median coverage: 75.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1 Euro-American (S-type) None 1.0
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 1.0
lineage4.4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB c.1321_1323delTCGinsGC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Leu464Met Mutation from literature
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.799C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761127 c.1321_1323delTCGinsGC frameshift_variant&missense_variant 0.21 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761196 p.Leu464Met missense_variant 0.13 rifampicin Mutation from literature
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
amikacin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.32 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761027 c.1221A>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761063 c.1257C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761088 c.1282_1284delAGCinsTCG synonymous_variant 0.24 rifampicin
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.21 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.2 rifampicin
rpoB 761132 c.1326G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761138 c.1332C>G synonymous_variant 0.22 rifampicin
rpoB 761150 c.1344A>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761156 c.1350G>C synonymous_variant 0.17 rifampicin
rpoB 761162 c.1356G>C synonymous_variant 0.14 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761168 c.1362C>G synonymous_variant 0.12 rifampicin
rpoB 761171 c.1365C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761174 c.1368T>A synonymous_variant 0.13 rifampicin
rpoB 761180 c.1374A>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761183 c.1377T>C synonymous_variant 0.13 rifampicin
rpoB 761186 p.Glu460Asp missense_variant 0.12 rifampicin Uncertain significance
rpoB 761195 c.1389G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.13 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.13 rifampicin
rpoB 761531 c.1725C>G synonymous_variant 0.15 rifampicin
rpoB 761534 c.1728G>C synonymous_variant 0.15 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761554 p.Val583Ala missense_variant 0.14 rifampicin Uncertain significance
rpoB 761564 c.1758G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761565 c.1759_1761delATGinsCC frameshift_variant&missense_variant 0.13 rifampicin
rpoB 761570 c.1764T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761600 c.1794T>C synonymous_variant 0.12 rifampicin
rpoB 761603 c.1797C>G synonymous_variant 0.11 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762878 p.Ile1024Met missense_variant 0.11 rifampicin
rpoB 762879 c.3073_3075delATGinsCC frameshift_variant&missense_variant 0.12 rifampicin
rpoB 762920 c.3114C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 762926 c.-444C>G upstream_gene_variant 0.13 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 762947 c.-423C>G upstream_gene_variant 0.12 rifampicin
rpoC 763468 c.99G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763483 c.114G>C synonymous_variant 0.19 rifampicin
rpoC 763486 c.117T>G synonymous_variant 0.19 rifampicin
rpoC 763504 c.135C>A synonymous_variant 0.26 rifampicin
rpoC 763507 c.138G>C synonymous_variant 0.26 rifampicin
rpoC 763528 c.159G>C synonymous_variant 0.29 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.29 rifampicin
rpoC 763537 c.168C>T synonymous_variant 0.29 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.28 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763622 c.253_255delGCCinsTG frameshift_variant&missense_variant 0.17 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.15 rifampicin
rpoC 763639 p.Glu90Asp missense_variant 0.15 rifampicin
rpoC 763642 c.273G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763669 c.300C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763708 c.339G>C synonymous_variant 0.2 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763732 c.363C>G synonymous_variant 0.16 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.12 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.12 rifampicin
rpoC 764359 c.990C>G synonymous_variant 0.13 rifampicin
rpoC 764371 c.1002G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764377 c.1008C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764387 c.1018_1020delTTGinsCC frameshift_variant&missense_variant 0.18 rifampicin
rpoC 764404 c.1035C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.17 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066A>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764441 p.Ile358Leu missense_variant 0.14 rifampicin
rpoC 764446 c.1077T>C synonymous_variant 0.15 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.15 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.15 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764485 c.1116G>C synonymous_variant 0.18 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764498 p.Ser377Ala missense_variant 0.17 rifampicin
rpoC 764507 p.Ala380Ser missense_variant 0.18 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764542 c.1173C>G synonymous_variant 0.2 rifampicin
rpoC 764548 c.1179G>C synonymous_variant 0.2 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>C synonymous_variant 0.22 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.24 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.23 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.26 rifampicin
rpoC 764641 c.1272C>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>C synonymous_variant 0.32 rifampicin
rpoC 764665 c.1296C>G synonymous_variant 0.31 rifampicin
rpoC 764668 c.1299C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.3 rifampicin
rpoC 764706 p.Leu446Gln missense_variant 0.27 rifampicin Uncertain significance
rpoC 764746 c.1377G>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764749 c.1380G>C synonymous_variant 0.23 rifampicin
rpoC 764758 c.1389C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764780 c.1411_1412delAGinsTC synonymous_variant 0.23 rifampicin
rpoC 764804 p.Gln479Phe missense_variant 0.2 rifampicin
rpoC 764809 c.1440C>T synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.2 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764818 c.1449G>C synonymous_variant 0.21 rifampicin
rpoC 764824 c.1455T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764833 c.1464A>G synonymous_variant 0.22 rifampicin
rpoC 764843 p.Ala492Thr missense_variant 0.21 rifampicin
rpoC 764857 c.1488G>C synonymous_variant 0.14 rifampicin
rpoC 764858 c.1489T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>C synonymous_variant 0.16 rifampicin
rpoC 764887 c.1518G>T synonymous_variant 0.11 rifampicin
rpoC 764888 c.1519T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.11 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472674 n.829T>A non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473022 n.1177G>A non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473292 n.1447_1449delGGAinsTGGG non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473317 n.1472G>A non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474125 n.468C>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474133 n.476T>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474141 n.484G>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474142 n.485C>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474155 n.498G>A non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474186 n.529A>T non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474451 n.794T>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474662 n.1005C>A non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474688 n.1031G>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1474710 n.1053T>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474711 n.1054_1055insAA non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474714 n.1058delT non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.48 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475688 n.2031G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475713 n.2056C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1475766 n.2109G>C non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475990 n.2333G>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid Uncertain significance
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.45 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834012 c.471G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834025 p.Gln162Ala missense_variant 0.11 pyrazinamide
rpsA 1834040 p.Lys167Gln missense_variant 0.11 pyrazinamide
rpsA 1834043 p.Glu168Lys missense_variant 0.11 pyrazinamide
rpsA 1834046 p.Ile169Leu missense_variant 0.11 pyrazinamide
rpsA 1834054 c.513C>G synonymous_variant 0.11 pyrazinamide
rpsA 1834294 c.753G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834298 p.Gln253Glu missense_variant 0.12 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.12 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834307 c.766_768delGACinsCG frameshift_variant&missense_variant 0.12 pyrazinamide Uncertain significance
rpsA 1834327 c.786G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834384 c.843A>G synonymous_variant 0.14 pyrazinamide
rpsA 1834395 p.Arg285Gln missense_variant 0.13 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834418 p.Ile293Leu missense_variant 0.13 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834427 p.Ile296Val missense_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834451 c.910_912delTTGinsCC frameshift_variant&missense_variant 0.12 pyrazinamide Uncertain significance
rpsA 1834456 c.915T>G synonymous_variant 0.11 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039988 c.717C>G synonymous_variant 0.13 pyrazinamide
clpC1 4039991 c.714G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039994 p.Glu237Asp missense_variant 0.13 pyrazinamide
clpC1 4040009 c.696C>G synonymous_variant 0.14 pyrazinamide
clpC1 4040015 c.690G>C synonymous_variant 0.13 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.16 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.17 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4040069 c.636G>C synonymous_variant 0.17 pyrazinamide
glpK 4139183 c.572dupG frameshift_variant 0.39 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin